BN1160 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.1772e-05 4.9523e-03
Layer 4 1.2349e-04 8.4639e-04
Layer 5 2.8199e-04 2.2911e-03
Layer 2 3.1802e-04 4.8979e-02
Layer 6 1.2321e-03 4.6948e-03
Layer 1 3.5866e-01 4.2207e-01
WM 9.4432e-01 5.8057e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
PRKAR1B Expression Distribution
Gene Specificity Score (GSS)
PRKAR1B GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
PRKAR1B Layer 5 2.4609 0.6960
AP2M1 Layer 6 2.4883 0.6908
TOLLIP Layer 5 2.4023 0.6838
ATP5F1A Layer 5 2.4941 0.6756
CFL1 Layer 4 2.3184 0.6754
DNM1 Layer 5 2.4941 0.6751
MORF4L1 Layer 5 2.3965 0.6738
ATP5F1D Layer 5 2.2676 0.6726
STMN2 Layer 4 2.7363 0.6707
TUBB Layer 6 2.5449 0.6697
STMN1 Layer 4 2.5059 0.6683
SLC22A17 Layer 4 2.5176 0.6676
HINT1 Layer 5 2.4180 0.6658
SNCA Layer 6 2.4395 0.6651
ARL6IP1 Layer 5 2.2676 0.6648
ATP6V1F Layer 4 2.2129 0.6645
TUBA1B Layer 5 1.9990 0.6644
CHGA Layer 4 3.0000 0.6635
BEX3 Layer 6 2.2832 0.6632
COX4I1 Layer 4 2.3086 0.6631
GHITM Layer 4 2.3711 0.6631
NDRG4 Layer 4 2.5176 0.6623
LMO4 Layer 4 2.6016 0.6597
KLC1 Layer 5 2.3398 0.6588
PPIA Layer 5 2.2031 0.6586
PCSK1N Layer 5 2.1777 0.6584
RTN1 Layer 4 2.3965 0.6562
TPI1 Layer 6 2.2617 0.6552
CALY Layer 5 2.3750 0.6537
GAP43 Layer 3 2.2832 0.6513
FKBP8 Layer 4 2.4395 0.6511
SNRPN Layer 5 2.5508 0.6508
COX5B Layer 4 2.2363 0.6501
CEND1 Layer 4 2.4609 0.6494
PPP2R1A Layer 5 2.3242 0.6486
NDUFB8 Layer 5 2.5332 0.6482
BEX5 Layer 4 2.4844 0.6476
SELENOW Layer 6 2.1289 0.6466
RPL8 Layer 5 2.2617 0.6459
MGST3 Layer 4 2.5273 0.6455
UQCRH Layer 5 2.3555 0.6450
BASP1 Layer 5 2.2227 0.6450
MAPK8IP2 Layer 4 2.4336 0.6442
MIF Layer 6 2.1973 0.6437
EEF1A2 Layer 5 2.4844 0.6431
COX7C Layer 4 2.2422 0.6422
RTN3 Layer 4 2.2227 0.6412
ENO2 Layer 4 2.5664 0.6409
THY1 Layer 6 2.3965 0.6406
SEZ6L2 Layer 4 2.6074 0.6402

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1160
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1160_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1160/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1160/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1160/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1160/report/PD/BN1160_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1160/report/PD/BN1160_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 02:34:50
  • Number of Processes: 10
  • Spending Time: 0h 2m